rs6850980

Variant names:

• chr4-113789138-A-G
• rs6850980

Your query was ambiguous. Multiple possible variants found:

• chr4-113789138-A-G
• chr4-113789138-A-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 0.306 in 151,894 control chromosomes in the GnomAD database, including 7,474 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 (7474 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 3 publications found

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 (SAS) allele frequency at 95% confidence interval = 0.482 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: 0.306 AC: 46384 AN: 151776 Hom.: 7475 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.306 AC: 46413 AN: 151894 Hom.: 7474 Cov.: 32 AF XY: 0.310 AC XY: 22976 AN XY: 74210

African (AFR) AF: 0.238 AC: 9851 AN: 41432

American (AMR) AF: 0.320 AC: 4884 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1034 AN: 3468

East Asian (EAS) AF: 0.477 AC: 2454 AN: 5146

South Asian (SAS) AF: 0.499 AC: 2404 AN: 4818

European-Finnish (FIN) AF: 0.316 AC: 3324 AN: 10532

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21517 AN: 67924

Other (OTH) AF: 0.308 AC: 649 AN: 2108

Alfa AF: 0.303 Hom.: 3044

Bravo AF: 0.299

Asia WGS AF: 0.472 AC: 1643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.48
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs6850980; hg19: chr4-114710294;