rs2161006

Variant names:

• chr5-31381407-C-T
• rs2161006

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 0.276 in 152,012 control chromosomes in the GnomAD database, including 6,766 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 0.28 (6766 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.358 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: 0.277 AC: 42015 AN: 151894 Hom.: 6762 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.276 AC: 42018 AN: 152012 Hom.: 6766 Cov.: 32 AF XY: 0.273 AC XY: 20296 AN XY: 74302

African (AFR) AF: 0.117 AC: 4847 AN: 41496

American (AMR) AF: 0.318 AC: 4854 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 956 AN: 3470

East Asian (EAS) AF: 0.247 AC: 1270 AN: 5150

South Asian (SAS) AF: 0.367 AC: 1768 AN: 4816

European-Finnish (FIN) AF: 0.250 AC: 2642 AN: 10558

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24617 AN: 67950

Other (OTH) AF: 0.310 AC: 651 AN: 2102

Alfa AF: 0.333 Hom.: 4834

Bravo AF: 0.278

Asia WGS AF: 0.303 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.39
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs2161006; hg19: chr5-31381514;