rs1800775

Variant names:

• chr16-56961324-C-A
• rs1800775

Your query was ambiguous. Multiple possible variants found:

• chr16-56961324-C-A
• chr16-56961324-C-G
• chr16-56961324-C-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 0.515 in 481,042 control chromosomes in the GnomAD database, including 64,531 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 0.52 (20884 hom., cov: 33)
  • Exomes 𝑓: 0.51 (43647 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 276 publications found

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 (SAS) allele frequency at 95% confidence interval = 0.582 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: 0.522 AC: 79285 AN: 151974 Hom.: 20854 Cov.: 33

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.502

GnomAD2 exomes AF: 0.508 AC: 88585 AN: 174424 AF XY: 0.511

Gnomad AFR exome AF: 0.558

Gnomad AMR exome AF: 0.528

Gnomad ASJ exome AF: 0.513

Gnomad EAS exome AF: 0.491

Gnomad FIN exome AF: 0.467

Gnomad NFE exome AF: 0.473

Gnomad OTH exome AF: 0.500

GnomAD4 exome AF: 0.512 AC: 168449 AN: 328950 Hom.: 43647 Cov.: 0 AF XY: 0.518 AC XY: 97232 AN XY: 187742

African (AFR) AF: 0.567 AC: 5509 AN: 9720

American (AMR) AF: 0.528 AC: 16390 AN: 31054

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 5702 AN: 11156

East Asian (EAS) AF: 0.500 AC: 5861 AN: 11726

South Asian (SAS) AF: 0.598 AC: 36785 AN: 61554

European-Finnish (FIN) AF: 0.490 AC: 7146 AN: 14598

Middle Eastern (MID) AF: 0.496 AC: 1378 AN: 2780

European-Non Finnish (NFE) AF: 0.479 AC: 82028 AN: 171172

Other (OTH) AF: 0.504 AC: 7650 AN: 15190

GnomAD4 genome AF: 0.522 AC: 79359 AN: 152092 Hom.: 20884 Cov.: 33 AF XY: 0.525 AC XY: 39066 AN XY: 74352

African (AFR) AF: 0.576 AC: 23875 AN: 41480

American (AMR) AF: 0.506 AC: 7738 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1748 AN: 3468

East Asian (EAS) AF: 0.498 AC: 2582 AN: 5180

South Asian (SAS) AF: 0.601 AC: 2897 AN: 4824

European-Finnish (FIN) AF: 0.509 AC: 5385 AN: 10572

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33337 AN: 67970

Other (OTH) AF: 0.502 AC: 1059 AN: 2110

Alfa AF: 0.499 Hom.: 85619

Bravo AF: 0.522

Asia WGS AF: 0.546 AC: 1902 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	0.41
DANN	Benign	0.66
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs1800775; hg19: chr16-56995236; COSMIC: COSV52363979;