rs951251

Variant names:

• chr6-131070072-G-A
• rs951251
• ENST00000754615.1:n.324+1062G>A

Variant summary

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

The ENST00000754615.1(ENSG00000298304):​n.324+1062G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,114 control chromosomes in the GnomAD database, including 2,308 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 0.15 (2308 hom., cov: 32)
• Consequence: ENSG00000298304 ENST00000754615.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• Publications: 8 publications found

Genes affected

ENSG00000298304 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000754615.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298304	ENST00000754615.1		n.324+1062G>A		intron	N/A
	ENSG00000298304	ENST00000754616.1		n.329-430G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22553 AN: 151996 Hom.: 2302 Cov.: 32

Gnomad AFR AF: 0.0367

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.148 AC: 22572 AN: 152114 Hom.: 2308 Cov.: 32 AF XY: 0.154 AC XY: 11454 AN XY: 74342

African (AFR) AF: 0.0367 AC: 1523 AN: 41552

American (AMR) AF: 0.162 AC: 2461 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 393 AN: 3468

East Asian (EAS) AF: 0.430 AC: 2217 AN: 5156

South Asian (SAS) AF: 0.220 AC: 1061 AN: 4816

European-Finnish (FIN) AF: 0.276 AC: 2910 AN: 10550

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11468 AN: 68014

Other (OTH) AF: 0.146 AC: 309 AN: 2114

Alfa AF: 0.168 Hom.: 1685

Bravo AF: 0.137

Asia WGS AF: 0.313 AC: 1087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.97
DANN	Benign	0.76
PhyloP100		-0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs951251;

hg19: chr6-131391212;