rs1016767

Variant names:

• chr4-82183862-G-A
• rs1016767

Your query was ambiguous. Multiple possible variants found:

• chr4-82183862-G-A
• chr4-82183862-G-T

Variant summary

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

The variant allele was found at a frequency of 0.264 in 152,158 control chromosomes in the GnomAD database, including 5,944 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 0.26 (5944 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.329 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

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40077 AN: 152040 Hom.: 5935 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.0997

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.264 AC: 40097 AN: 152158 Hom.: 5944 Cov.: 32 AF XY: 0.265 AC XY: 19687 AN XY: 74370

African (AFR) AF: 0.153 AC: 6353 AN: 41552

American (AMR) AF: 0.193 AC: 2952 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1147 AN: 3472

East Asian (EAS) AF: 0.0999 AC: 517 AN: 5174

South Asian (SAS) AF: 0.319 AC: 1540 AN: 4822

European-Finnish (FIN) AF: 0.372 AC: 3932 AN: 10558

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22628 AN: 67980

Other (OTH) AF: 0.263 AC: 555 AN: 2114

Alfa AF: 0.261 Hom.: 2448

Bravo AF: 0.241

Asia WGS AF: 0.208 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.47
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs1016767; hg19: chr4-83105015;