rs1364225

Variant names:

• chr16-86509420-C-G
• rs1364225

Your query was ambiguous. Multiple possible variants found:

• chr16-86509420-C-G
• chr16-86509420-C-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 0.683 in 152,236 control chromosomes in the GnomAD database, including 36,747 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 0.68 (36747 hom., cov: 36)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 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: 0.683 AC: 103897 AN: 152118 Hom.: 36720 Cov.: 36

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.683 AC: 103978 AN: 152236 Hom.: 36747 Cov.: 36 AF XY: 0.688 AC XY: 51190 AN XY: 74438

African (AFR) AF: 0.487 AC: 20227 AN: 41536

American (AMR) AF: 0.801 AC: 12254 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2728 AN: 3472

East Asian (EAS) AF: 0.865 AC: 4464 AN: 5158

South Asian (SAS) AF: 0.679 AC: 3284 AN: 4834

European-Finnish (FIN) AF: 0.779 AC: 8266 AN: 10616

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.742 AC: 50426 AN: 67998

Other (OTH) AF: 0.718 AC: 1514 AN: 2110

Alfa AF: 0.704 Hom.: 4759

Bravo AF: 0.680

Asia WGS AF: 0.753 AC: 2618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	7.5
DANN	Benign	0.76
PhyloP100		-0.094

Splicing

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

Other links and lift over

dbSNP: rs1364225; hg19: chr16-86543026;