rs916331

Variant names:

• chr6-167057071-T-G
• rs916331
• ENST00000705249.1:c.1065+23100T>G

Variant summary

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

The ENST00000705249.1(ENSG00000272980):​c.1065+23100T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,078 control chromosomes in the GnomAD database, including 8,189 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 0.31 (8189 hom., cov: 32)
• Consequence: ENSG00000272980 ENST00000705249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

Genes affected

ENSG00000272980 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 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
ENSG00000272980	ENST00000705249.1	c.1065+23100T>G		intron_variant	Intron 11 of 12			ENSP00000516101.1

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47433 AN: 151960 Hom.: 8188 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.312 AC: 47428 AN: 152078 Hom.: 8189 Cov.: 32 AF XY: 0.311 AC XY: 23144 AN XY: 74344

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.314

Alfa AF: 0.350 Hom.: 1239

Bravo AF: 0.298

Asia WGS AF: 0.263 AC: 918 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	3.5
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs916331; hg19: chr6-167470559;