chr14-51453104-A-G

Variant names:

• chr14-51453104-A-G
• rs7153703
• XM_047430921.1:c.-290+20642A>G

Variant summary

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

The ENST00000697566.1(FRMD6-AS2):​n.119-60055T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 151,868 control chromosomes in the GnomAD database, including 4,776 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 0.24 (4776 hom., cov: 31)
• Consequence: FRMD6-AS2 ENST00000697566.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.713
• Publications: 3 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000697566.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRMD6-AS2	ENST00000697566.1		n.119-60055T>C		intron	N/A
	FRMD6-AS2	ENST00000697567.1		n.265-60055T>C		intron	N/A
	FRMD6-AS2	ENST00000697568.1		n.260-55984T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36865 AN: 151750 Hom.: 4782 Cov.: 31

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.243 AC: 36874 AN: 151868 Hom.: 4776 Cov.: 31 AF XY: 0.243 AC XY: 18018 AN XY: 74200

African (AFR) AF: 0.315 AC: 13029 AN: 41398

American (AMR) AF: 0.227 AC: 3470 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3466

East Asian (EAS) AF: 0.153 AC: 791 AN: 5172

South Asian (SAS) AF: 0.303 AC: 1456 AN: 4804

European-Finnish (FIN) AF: 0.254 AC: 2669 AN: 10514

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13899 AN: 67954

Other (OTH) AF: 0.228 AC: 479 AN: 2102

Alfa AF: 0.208 Hom.: 11908

Bravo AF: 0.243

Asia WGS AF: 0.262 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.9
DANN	Benign	0.86
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs7153703; hg19: chr14-51919822;