rs6953751

Positions:

• chr7-155584735-T-C
• chr7-155584735-T-G

Variant summary

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

The ENST00000688916.1(ENSG00000283128):​c.-298-7902A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 152,058 control chromosomes in the GnomAD database, including 34,143 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 0.67 (34143 hom., cov: 32)
• Consequence: ENST00000688916.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.51

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000688916.1	c.-298-7902A>G		intron_variant				ENSP00000510525	P1

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101339 AN: 151938 Hom.: 34114 Cov.: 32

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.667 AC: 101428 AN: 152058 Hom.: 34143 Cov.: 32 AF XY: 0.668 AC XY: 49622 AN XY: 74320

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.688

Alfa AF: 0.693 Hom.: 74992

Bravo AF: 0.658

Asia WGS AF: 0.618 AC: 2152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6953751; hg19: chr7-155377430;