9-38704683-C-T

Variant names:

• chr9-38704683-C-T
• rs4557782
• NM_001394922.1:c.-3-681G>A

Variant summary

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

The NM_001394922.1(FAM240B):​c.-3-681G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.855 in 152,194 control chromosomes in the GnomAD database, including 55,874 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 0.86 (55874 hom., cov: 32)
• Consequence: FAM240B NM_001394922.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 4 publications found

Genes affected

FAM240B (HGNC:53430): (family with sequence similarity 240 member B)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM240B	NM_001394922.1	c.-3-681G>A		intron_variant	Intron 1 of 2	ENST00000637493.2	NP_001381851.1
FAM240B	NM_001386811.1	c.-4+647G>A		intron_variant	Intron 1 of 2		NP_001373740.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM240B	ENST00000637493.2	c.-3-681G>A		intron_variant	Intron 1 of 2	5	NM_001394922.1	ENSP00000490097.1
FAM240B	ENST00000637691.1	c.-4+647G>A		intron_variant	Intron 1 of 2	5		ENSP00000490707.1

Frequencies

GnomAD3 genomes AF: 0.855 AC: 130075 AN: 152076 Hom.: 55817 Cov.: 32

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.851

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.855 AC: 130189 AN: 152194 Hom.: 55874 Cov.: 32 AF XY: 0.854 AC XY: 63499 AN XY: 74394

African (AFR) AF: 0.902 AC: 37488 AN: 41544

American (AMR) AF: 0.792 AC: 12110 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2853 AN: 3472

East Asian (EAS) AF: 0.691 AC: 3565 AN: 5162

South Asian (SAS) AF: 0.887 AC: 4270 AN: 4814

European-Finnish (FIN) AF: 0.850 AC: 9003 AN: 10592

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58125 AN: 68008

Other (OTH) AF: 0.852 AC: 1798 AN: 2110

Alfa AF: 0.850 Hom.: 93315

Bravo AF: 0.849

Asia WGS AF: 0.846 AC: 2939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.15
DANN	Benign	0.64
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4557782; hg19: chr9-38704680; COSMIC: COSV60354752;