chr6-131070072-G-A

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378004	XR_942993.3	n.331+1062G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298304	ENST00000754615.1	n.324+1062G>A		intron_variant	Intron 2 of 2
ENSG00000298304	ENST00000754616.1	n.329-430G>A		intron_variant	Intron 2 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs951251; hg19: chr6-131391212;