rs3897510

Variant names:

• chr20-6148621-A-C
• rs3897510

Your query was ambiguous. Multiple possible variants found:

• chr20-6148621-A-C
• chr20-6148621-A-G
• chr20-6148621-A-T

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 0.321 in 152,068 control chromosomes in the GnomAD database, including 8,045 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 0.32 (8045 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 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: 0.321 AC: 48748 AN: 151950 Hom.: 8046 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.321 AC: 48755 AN: 152068 Hom.: 8045 Cov.: 32 AF XY: 0.317 AC XY: 23533 AN XY: 74346

African (AFR) AF: 0.275 AC: 11403 AN: 41484

American (AMR) AF: 0.265 AC: 4056 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1416 AN: 3472

East Asian (EAS) AF: 0.320 AC: 1653 AN: 5162

South Asian (SAS) AF: 0.204 AC: 983 AN: 4820

European-Finnish (FIN) AF: 0.330 AC: 3492 AN: 10580

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24652 AN: 67962

Other (OTH) AF: 0.319 AC: 671 AN: 2102

Alfa AF: 0.339 Hom.: 16579

Bravo AF: 0.316

Asia WGS AF: 0.248 AC: 862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	12
DANN	Benign	0.85
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs3897510; hg19: chr20-6129268;