20-6641038-C-T

Variant names:

• chr20-6641038-C-T
• rs2145270

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 0.615 in 151,792 control chromosomes in the GnomAD database, including 29,408 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 0.62 (29408 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 36 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 (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93269 AN: 151674 Hom.: 29368 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.615 AC: 93364 AN: 151792 Hom.: 29408 Cov.: 31 AF XY: 0.620 AC XY: 45980 AN XY: 74168

African (AFR) AF: 0.508 AC: 21005 AN: 41334

American (AMR) AF: 0.718 AC: 10960 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1939 AN: 3466

East Asian (EAS) AF: 0.892 AC: 4596 AN: 5154

South Asian (SAS) AF: 0.546 AC: 2620 AN: 4800

European-Finnish (FIN) AF: 0.696 AC: 7336 AN: 10540

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42834 AN: 67924

Other (OTH) AF: 0.614 AC: 1296 AN: 2110

Alfa AF: 0.632 Hom.: 94714

Bravo AF: 0.615

Asia WGS AF: 0.685 AC: 2383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.017
DANN	Benign	0.65
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2145270; hg19: chr20-6621685;