rs6953751

Variant names:

• chr7-155584735-T-C
• rs6953751
• ENST00000688916.1:c.-298-7902A>G

Your query was ambiguous. Multiple possible variants found:

• 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: ENSG00000283128 ENST00000688916.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.51

Genes affected

ENSG00000283128 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283128	ENST00000688916.1	c.-298-7902A>G		intron_variant	Intron 2 of 6			ENSP00000510525.1

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;