NM_001394922.1:c.-4+6938G>A

Variant names:

• chr9-38713084-C-T
• rs12686281
• NM_001394922.1:c.-4+6938G>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.-4+6938G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0886 in 152,206 control chromosomes in the GnomAD database, including 606 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 0.089 (606 hom., cov: 31)
• Consequence: FAM240B NM_001394922.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 0 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394922.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM240B	NM_001394922.1	MANE Select	c.-4+6938G>A		intron	N/A	NP_001381851.1	A0A1B0GVZ2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM240B	ENST00000637493.2	TSL:5 MANE Select	c.-4+6938G>A		intron	N/A	ENSP00000490097.1	A0A1B0GVZ2

Frequencies

GnomAD3 genomes AF: 0.0886 AC: 13482 AN: 152088 Hom.: 605 Cov.: 31

Gnomad AFR AF: 0.0759

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0969

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.0578

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0675

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0920

Gnomad OTH AF: 0.0979

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

GnomAD4 genome AF: 0.0886 AC: 13487 AN: 152206 Hom.: 606 Cov.: 31 AF XY: 0.0880 AC XY: 6552 AN XY: 74414

African (AFR) AF: 0.0758 AC: 3148 AN: 41528

American (AMR) AF: 0.0969 AC: 1482 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 623 AN: 3472

East Asian (EAS) AF: 0.0581 AC: 300 AN: 5164

South Asian (SAS) AF: 0.133 AC: 640 AN: 4824

European-Finnish (FIN) AF: 0.0675 AC: 715 AN: 10600

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0920 AC: 6256 AN: 68002

Other (OTH) AF: 0.0964 AC: 204 AN: 2116

Alfa AF: 0.0915 Hom.: 1171

Bravo AF: 0.0883

Asia WGS AF: 0.0850 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.8
DANN	Benign	0.62
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs12686281; hg19: chr9-38713081;