chr20-6797517-A-G

Variant names:

• chr20-6797517-A-G
• rs235739

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 0.423 in 152,010 control chromosomes in the GnomAD database, including 14,597 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 0.42 (14597 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 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: 0.423 AC: 64313 AN: 151892 Hom.: 14579 Cov.: 32

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.423 AC: 64369 AN: 152010 Hom.: 14597 Cov.: 32 AF XY: 0.424 AC XY: 31523 AN XY: 74292

African (AFR) AF: 0.591 AC: 24510 AN: 41462

American (AMR) AF: 0.430 AC: 6576 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1153 AN: 3468

East Asian (EAS) AF: 0.543 AC: 2806 AN: 5166

South Asian (SAS) AF: 0.357 AC: 1722 AN: 4818

European-Finnish (FIN) AF: 0.337 AC: 3553 AN: 10552

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22766 AN: 67956

Other (OTH) AF: 0.418 AC: 881 AN: 2108

Alfa AF: 0.363 Hom.: 20497

Bravo AF: 0.439

Asia WGS AF: 0.439 AC: 1528 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.8
DANN	Benign	0.83
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs235739; hg19: chr20-6778164;