rs7153703

chr14-51453104-A-Gchr14-51453104-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000697567.1(FRMD6-AS2):n.265-60055T>C variant causes a intron, non coding transcript 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 ENST00000697567.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.713

Genes affected

FRMD6-AS2 (HGNC:43637): (FRMD6 antisense RNA 2)

FRMD6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FRMD6	XM_047430921.1	c.-290+20642A>G		intron_variant
FRMD6	XM_047430922.1	c.-290+20611A>G		intron_variant
FRMD6	XM_047430926.1	c.-393+20642A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FRMD6-AS2	ENST00000697567.1	n.265-60055T>C		intron_variant, non_coding_transcript_variant
FRMD6-AS2	ENST00000697566.1	n.119-60055T>C		intron_variant, non_coding_transcript_variant
FRMD6-AS2	ENST00000697568.1	n.260-55984T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.228

Alfa AF: 0.198 Hom.: 4582

Bravo AF: 0.243

Asia WGS AF: 0.262 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	8.9
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7153703; hg19: chr14-51919822;