rs7140150

Variant names:

• chr14-51544081-C-T
• rs7140150
• ENST00000356218.8:c.-209-26267C>T

Variant summary

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

The ENST00000356218.8(FRMD6):​c.-209-26267C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,200 control chromosomes in the GnomAD database, including 23,416 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 0.55 (23416 hom., cov: 31)
• Consequence: FRMD6 ENST00000356218.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 10 publications found

Genes affected

FRMD6 (HGNC:19839): (FERM domain containing 6) Predicted to be involved in actomyosin structure organization. Predicted to act upstream of or within apical constriction; cellular protein localization; and regulation of actin filament-based process. Predicted to be located in apical junction complex. Predicted to be active in cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

FRMD6-AS2 (HGNC:43637): (FRMD6 antisense RNA 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRMD6	NM_001042481.3	c.-209-26267C>T		intron_variant	Intron 1 of 14		NP_001035946.1
FRMD6-AS2	NR_051990.1	n.244+40085G>A		intron_variant	Intron 2 of 2
FRMD6	XM_011536424.2	c.-209-26267C>T		intron_variant	Intron 2 of 15		XP_011534726.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FRMD6	ENST00000356218.8	c.-209-26267C>T		intron_variant	Intron 1 of 14	1		ENSP00000348550.4
FRMD6	ENST00000556137.5	n.446-26267C>T		intron_variant	Intron 2 of 3	4
FRMD6-AS2	ENST00000556617.5	n.244+40085G>A		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.555 AC: 83825 AN: 151086 Hom.: 23398 Cov.: 31

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.410

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.555 AC: 83889 AN: 151200 Hom.: 23416 Cov.: 31 AF XY: 0.558 AC XY: 41189 AN XY: 73854

African (AFR) AF: 0.562 AC: 23144 AN: 41192

American (AMR) AF: 0.564 AC: 8563 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3468

East Asian (EAS) AF: 0.502 AC: 2581 AN: 5146

South Asian (SAS) AF: 0.578 AC: 2774 AN: 4802

European-Finnish (FIN) AF: 0.586 AC: 6128 AN: 10456

Middle Eastern (MID) AF: 0.410 AC: 119 AN: 290

European-Non Finnish (NFE) AF: 0.558 AC: 37738 AN: 67658

Other (OTH) AF: 0.514 AC: 1081 AN: 2102

Alfa AF: 0.553 Hom.: 59902

Bravo AF: 0.552

Asia WGS AF: 0.573 AC: 1994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.070
DANN	Benign	0.24
PhyloP100		-1.6
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: rs7140150; hg19: chr14-52010799;