rs4238595

Variant names:

• chr16-20331769-T-C
• rs4238595

Your query was ambiguous. Multiple possible variants found:

• chr16-20331769-T-C
• chr16-20331769-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 0.775 in 152,208 control chromosomes in the GnomAD database, including 46,951 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 0.78 (46951 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 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: 0.775 AC: 117897 AN: 152090 Hom.: 46891 Cov.: 33

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.775 AC: 118011 AN: 152208 Hom.: 46951 Cov.: 33 AF XY: 0.773 AC XY: 57521 AN XY: 74402

African (AFR) AF: 0.943 AC: 39209 AN: 41562

American (AMR) AF: 0.685 AC: 10481 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2644 AN: 3472

East Asian (EAS) AF: 0.992 AC: 5142 AN: 5182

South Asian (SAS) AF: 0.849 AC: 4094 AN: 4820

European-Finnish (FIN) AF: 0.675 AC: 7138 AN: 10580

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46884 AN: 67986

Other (OTH) AF: 0.766 AC: 1618 AN: 2112

Alfa AF: 0.711 Hom.: 75324

Bravo AF: 0.784

Asia WGS AF: 0.914 AC: 3181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.31
DANN	Benign	0.79
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4238595; hg19: chr16-20343091;