NM_022763.4:c.1971+100G>A

Variant names:

• chr3-172341331-G-A
• rs570549
• NM_022763.4:c.1971+100G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022763.4(FNDC3B):​c.1971+100G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 861,140 control chromosomes in the GnomAD database, including 205,040 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.64 (32295 hom., cov: 33)
  • Exomes 𝑓: 0.69 (172745 hom.)
• Consequence: FNDC3B NM_022763.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.866
• Publications: 7 publications found

Genes affected

FNDC3B (HGNC:24670): (fibronectin type III domain containing 3B) Enables RNA binding activity. Predicted to act upstream of or within several processes, including negative regulation of osteoblast differentiation; substrate adhesion-dependent cell spreading; and type II pneumocyte differentiation. Predicted to be located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FNDC3B	NM_022763.4	c.1971+100G>A		intron_variant	Intron 17 of 25	ENST00000415807.7	NP_073600.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FNDC3B	ENST00000415807.7	c.1971+100G>A		intron_variant	Intron 17 of 25	1	NM_022763.4	ENSP00000411242.2
FNDC3B	ENST00000336824.8	c.1971+100G>A		intron_variant	Intron 17 of 25	1		ENSP00000338523.4
FNDC3B	ENST00000416957.5	c.1971+100G>A		intron_variant	Intron 17 of 25	1		ENSP00000389094.1

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97541 AN: 151974 Hom.: 32271 Cov.: 33

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.605

GnomAD4 exome AF: 0.695 AC: 492774 AN: 709048 Hom.: 172745 AF XY: 0.691 AC XY: 261933 AN XY: 378978

African (AFR) AF: 0.470 AC: 9013 AN: 19194

American (AMR) AF: 0.777 AC: 33566 AN: 43198

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 13646 AN: 20948

East Asian (EAS) AF: 0.827 AC: 29706 AN: 35928

South Asian (SAS) AF: 0.629 AC: 43766 AN: 69600

European-Finnish (FIN) AF: 0.691 AC: 33418 AN: 48364

Middle Eastern (MID) AF: 0.528 AC: 2046 AN: 3872

European-Non Finnish (NFE) AF: 0.702 AC: 303691 AN: 432430

Other (OTH) AF: 0.674 AC: 23922 AN: 35514

GnomAD4 genome AF: 0.642 AC: 97598 AN: 152092 Hom.: 32295 Cov.: 33 AF XY: 0.643 AC XY: 47805 AN XY: 74340

African (AFR) AF: 0.479 AC: 19859 AN: 41456

American (AMR) AF: 0.709 AC: 10834 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2190 AN: 3468

East Asian (EAS) AF: 0.815 AC: 4225 AN: 5182

South Asian (SAS) AF: 0.639 AC: 3086 AN: 4826

European-Finnish (FIN) AF: 0.702 AC: 7416 AN: 10560

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47878 AN: 68000

Other (OTH) AF: 0.609 AC: 1287 AN: 2114

Alfa AF: 0.677 Hom.: 61305

Bravo AF: 0.637

Asia WGS AF: 0.712 AC: 2475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.32
DANN	Benign	0.76
PhyloP100		-0.87
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs570549; hg19: chr3-172059121;