rs1041756

Variant names:

• chr21-31866687-T-C
• rs1041756

Your query was ambiguous. Multiple possible variants found:

• chr21-31866687-T-C
• chr21-31866687-T-G

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 0.376 in 152,092 control chromosomes in the GnomAD database, including 11,642 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 0.38 (11642 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.48 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: 0.376 AC: 57204 AN: 151974 Hom.: 11621 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.0567

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.376 AC: 57258 AN: 152092 Hom.: 11642 Cov.: 32 AF XY: 0.371 AC XY: 27619 AN XY: 74348

African (AFR) AF: 0.485 AC: 20119 AN: 41450

American (AMR) AF: 0.269 AC: 4114 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1512 AN: 3470

East Asian (EAS) AF: 0.0568 AC: 294 AN: 5174

South Asian (SAS) AF: 0.269 AC: 1297 AN: 4818

European-Finnish (FIN) AF: 0.364 AC: 3852 AN: 10584

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24937 AN: 67988

Other (OTH) AF: 0.361 AC: 762 AN: 2108

Alfa AF: 0.284 Hom.: 1015

Bravo AF: 0.372

Asia WGS AF: 0.197 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.44
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs1041756; hg19: chr21-33239000;