1-206985344-A-T

Variant names:

• chr1-206985344-A-T
• rs2842711

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 0.462 in 152,020 control chromosomes in the GnomAD database, including 18,177 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 0.46 (18177 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.706 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: 0.461 AC: 70062 AN: 151902 Hom.: 18129 Cov.: 32

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.462 AC: 70176 AN: 152020 Hom.: 18177 Cov.: 32 AF XY: 0.455 AC XY: 33842 AN XY: 74320

African (AFR) AF: 0.713 AC: 29550 AN: 41460

American (AMR) AF: 0.446 AC: 6809 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1663 AN: 3468

East Asian (EAS) AF: 0.425 AC: 2201 AN: 5174

South Asian (SAS) AF: 0.202 AC: 973 AN: 4816

European-Finnish (FIN) AF: 0.299 AC: 3160 AN: 10562

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24320 AN: 67950

Other (OTH) AF: 0.490 AC: 1033 AN: 2110

Alfa AF: 0.413 Hom.: 1769

Bravo AF: 0.485

Asia WGS AF: 0.329 AC: 1145 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	9.3
DANN	Benign	0.82
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs2842711; hg19: chr1-207158689;