chr14-51497551-A-G

Variant names:

• chr14-51497551-A-G
• rs10150152
• ENST00000356218.8:c.-210+8131A>G

Variant summary

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

The ENST00000356218.8(FRMD6):​c.-210+8131A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 152,018 control chromosomes in the GnomAD database, including 18,792 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 0.49 (18792 hom., cov: 32)
• Consequence: FRMD6 ENST00000356218.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.75
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRMD6	NM_001042481.3	c.-210+8131A>G		intron_variant	Intron 1 of 14		NP_001035946.1
FRMD6-AS2	NR_051990.1	n.245-42736T>C		intron_variant	Intron 2 of 2
FRMD6	XM_011536424.2	c.-210+6017A>G		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.-210+8131A>G		intron_variant	Intron 1 of 14	1		ENSP00000348550.4
FRMD6	ENST00000556137.5	n.445+6017A>G		intron_variant	Intron 2 of 3	4
FRMD6-AS2	ENST00000556617.5	n.245-42736T>C		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74189 AN: 151900 Hom.: 18752 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.489 AC: 74288 AN: 152018 Hom.: 18792 Cov.: 32 AF XY: 0.491 AC XY: 36507 AN XY: 74290

African (AFR) AF: 0.578 AC: 23970 AN: 41464

American (AMR) AF: 0.560 AC: 8547 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1250 AN: 3472

East Asian (EAS) AF: 0.648 AC: 3351 AN: 5172

South Asian (SAS) AF: 0.600 AC: 2886 AN: 4812

European-Finnish (FIN) AF: 0.381 AC: 4029 AN: 10562

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28726 AN: 67968

Other (OTH) AF: 0.470 AC: 993 AN: 2112

Alfa AF: 0.442 Hom.: 25524

Bravo AF: 0.503

Asia WGS AF: 0.645 AC: 2241 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.031
DANN	Benign	0.48
PhyloP100		-2.8
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: rs10150152; hg19: chr14-51964269;