rs7272098

Variant names:

• chr20-17686606-T-A
• rs7272098

Your query was ambiguous. Multiple possible variants found:

• chr20-17686606-T-A
• chr20-17686606-T-C
• chr20-17686606-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 0.354 in 152,070 control chromosomes in the GnomAD database, including 9,961 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 0.35 (9961 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.642 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: 0.354 AC: 53804 AN: 151952 Hom.: 9945 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.354 AC: 53854 AN: 152070 Hom.: 9961 Cov.: 32 AF XY: 0.358 AC XY: 26622 AN XY: 74308

African (AFR) AF: 0.287 AC: 11909 AN: 41494

American (AMR) AF: 0.346 AC: 5282 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3470

East Asian (EAS) AF: 0.661 AC: 3416 AN: 5170

South Asian (SAS) AF: 0.406 AC: 1956 AN: 4814

European-Finnish (FIN) AF: 0.415 AC: 4382 AN: 10568

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25099 AN: 67960

Other (OTH) AF: 0.335 AC: 708 AN: 2112

Alfa AF: 0.362 Hom.: 1272

Bravo AF: 0.347

Asia WGS AF: 0.425 AC: 1473 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	3.5
DANN	Benign	0.77
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs7272098; hg19: chr20-17667251;