rs10150152

Positions:

• chr14-51497551-A-G
• chr14-51497551-A-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
FRMD6-AS2	NR_051990.1	n.245-42736T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FRMD6-AS2	ENST00000697567.1	n.264+86615T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.470

Alfa AF: 0.437 Hom.: 19971

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

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: rs10150152; hg19: chr14-51964269;