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. The variant received -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
• Publications: 6 publications found

Genes affected

ENSG00000283128 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000688916.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283128	ENST00000688916.1		c.-298-7902A>G		intron	N/A	ENSP00000510525.1
	ENSG00000283128	ENST00000635770.1	TSL:5	n.321-7902A>G		intron	N/A
	ENSG00000283128	ENST00000635903.1	TSL:5	n.30+782A>G		intron	N/A

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

African (AFR) AF: 0.607 AC: 25157 AN: 41472

American (AMR) AF: 0.703 AC: 10737 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2442 AN: 3472

East Asian (EAS) AF: 0.527 AC: 2723 AN: 5164

South Asian (SAS) AF: 0.653 AC: 3135 AN: 4804

European-Finnish (FIN) AF: 0.705 AC: 7457 AN: 10580

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47602 AN: 67968

Other (OTH) AF: 0.688 AC: 1456 AN: 2116

Alfa AF: 0.687 Hom.: 157939

Bravo AF: 0.658

Asia WGS AF: 0.618 AC: 2152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.32
PhyloP100		-4.5

Splicing

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

Other links and lift over

dbSNP: rs6953751; hg19: chr7-155377430;