rs7172340

Variant names:

• chr15-68288463-G-A
• rs7172340
• NM_015322.5:c.249-1144G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015322.5(FEM1B):​c.249-1144G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.969 in 152,336 control chromosomes in the GnomAD database, including 71,489 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 0.97 (71489 hom., cov: 32)
• Consequence: FEM1B NM_015322.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224

Genes affected

FEM1B (HGNC:3649): (fem-1 homolog B) This gene encodes an ankyrin repeat protein that belongs to the death receptor-associated family of proteins and plays a role in mediating apoptosis. The encoded protein is also thought to function in the replication stress-induced checkpoint signaling pathway via interaction with checkpoint kinase 1. [provided by RefSeq, Aug 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FEM1B	NM_015322.5	c.249-1144G>A		intron_variant	Intron 1 of 1	ENST00000306917.5	NP_056137.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FEM1B	ENST00000306917.5	c.249-1144G>A		intron_variant	Intron 1 of 1	1	NM_015322.5	ENSP00000307298.4
FEM1B	ENST00000570067.1	c.-226-1144G>A		intron_variant	Intron 1 of 1	4		ENSP00000457002.1

Frequencies

GnomAD3 genomes AF: 0.969 AC: 147443 AN: 152218 Hom.: 71437 Cov.: 32

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.960

Gnomad ASJ AF: 0.977

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.972

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.965

Gnomad OTH AF: 0.971

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

GnomAD4 genome AF: 0.969 AC: 147555 AN: 152336 Hom.: 71489 Cov.: 32 AF XY: 0.969 AC XY: 72176 AN XY: 74496

Gnomad4 AFR AF: 0.975

Gnomad4 AMR AF: 0.961

Gnomad4 ASJ AF: 0.977

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.971

Gnomad4 FIN AF: 0.958

Gnomad4 NFE AF: 0.965

Gnomad4 OTH AF: 0.972

Alfa AF: 0.966 Hom.: 91907

Bravo AF: 0.970

Asia WGS AF: 0.975 AC: 3393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.31
DANN	Benign	0.21

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

Publications

LitVar

Other links and lift over

dbSNP: rs7172340; hg19: chr15-68580801;