chr14-51534172-C-T

Variant names:

• chr14-51534172-C-T
• rs9323211
• ENST00000356218.8:c.-209-36176C>T

Variant summary

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

The NM_001042481.3(FRMD6):​c.-209-36176C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 152,078 control chromosomes in the GnomAD database, including 10,451 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 0.36 (10451 hom., cov: 32)
• Consequence: FRMD6 NM_001042481.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001042481.3. 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
	FRMD6	NM_001042481.3		c.-209-36176C>T		intron	N/A	NP_001035946.1	Q96NE9-2
	FRMD6-AS2	NR_051990.1		n.244+49994G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRMD6	ENST00000356218.8	TSL:1	c.-209-36176C>T		intron	N/A	ENSP00000348550.4	Q96NE9-2
	FRMD6	ENST00000556137.5	TSL:4	n.446-36176C>T		intron	N/A
	FRMD6-AS2	ENST00000556617.5	TSL:4	n.244+49994G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54581 AN: 151960 Hom.: 10446 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.359 AC: 54617 AN: 152078 Hom.: 10451 Cov.: 32 AF XY: 0.356 AC XY: 26448 AN XY: 74332

African (AFR) AF: 0.505 AC: 20958 AN: 41462

American (AMR) AF: 0.340 AC: 5192 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 971 AN: 3472

East Asian (EAS) AF: 0.284 AC: 1472 AN: 5178

South Asian (SAS) AF: 0.343 AC: 1654 AN: 4816

European-Finnish (FIN) AF: 0.210 AC: 2226 AN: 10580

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21140 AN: 67970

Other (OTH) AF: 0.337 AC: 712 AN: 2112

Alfa AF: 0.341 Hom.: 1532

Bravo AF: 0.373

Asia WGS AF: 0.325 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.56
PhyloP100		-0.34
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: rs9323211; hg19: chr14-52000890;