rs11626565

Variant names:

• chr14-51608434-A-C
• rs11626565
• ENST00000356218.8:c.-147+38024A>C

Your query was ambiguous. Multiple possible variants found:

• chr14-51608434-A-C
• chr14-51608434-A-T

Variant summary

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

The ENST00000356218.8(FRMD6):​c.-147+38024A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,234 control chromosomes in the GnomAD database, including 1,074 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 0.10 (1074 hom., cov: 32)
• Consequence: FRMD6 ENST00000356218.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000356218.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRMD6	NM_001042481.3		c.-147+38024A>C		intron	N/A	NP_001035946.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRMD6	ENST00000356218.8	TSL:1	c.-147+38024A>C		intron	N/A	ENSP00000348550.4
	FRMD6	ENST00000554745.1	TSL:4	n.278-35018A>C		intron	N/A
	FRMD6	ENST00000556137.5	TSL:4	n.508+38024A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15584 AN: 152116 Hom.: 1074 Cov.: 32

Gnomad AFR AF: 0.0264

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0730

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0219

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.102 AC: 15585 AN: 152234 Hom.: 1074 Cov.: 32 AF XY: 0.102 AC XY: 7571 AN XY: 74418

African (AFR) AF: 0.0264 AC: 1097 AN: 41536

American (AMR) AF: 0.0729 AC: 1116 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 606 AN: 3472

East Asian (EAS) AF: 0.0218 AC: 113 AN: 5182

South Asian (SAS) AF: 0.130 AC: 629 AN: 4820

European-Finnish (FIN) AF: 0.143 AC: 1517 AN: 10590

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10164 AN: 68016

Other (OTH) AF: 0.107 AC: 225 AN: 2112

Alfa AF: 0.124 Hom.: 2790

Bravo AF: 0.0928

Asia WGS AF: 0.0630 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.59
PhyloP100		-0.26
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: rs11626565; hg19: chr14-52075152;