rs2381416

Variant names:

• chr9-6193455-C-A
• rs2381416

Your query was ambiguous. Multiple possible variants found:

• chr9-6193455-C-A
• chr9-6193455-C-G
• chr9-6193455-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 0.662 in 151,912 control chromosomes in the GnomAD database, including 35,033 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 0.66 (35033 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 45 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 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: 0.663 AC: 100571 AN: 151794 Hom.: 35028 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.662 AC: 100606 AN: 151912 Hom.: 35033 Cov.: 32 AF XY: 0.665 AC XY: 49380 AN XY: 74270

African (AFR) AF: 0.433 AC: 17933 AN: 41384

American (AMR) AF: 0.750 AC: 11465 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2318 AN: 3470

East Asian (EAS) AF: 0.955 AC: 4939 AN: 5172

South Asian (SAS) AF: 0.761 AC: 3665 AN: 4814

European-Finnish (FIN) AF: 0.734 AC: 7735 AN: 10544

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50346 AN: 67934

Other (OTH) AF: 0.680 AC: 1433 AN: 2108

Alfa AF: 0.720 Hom.: 120500

Bravo AF: 0.650

Asia WGS AF: 0.819 AC: 2844 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.64
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs2381416; hg19: chr9-6193455;