rs366905

Variant names:

• chr6-149413961-T-A
• rs366905

Your query was ambiguous. Multiple possible variants found:

• chr6-149413961-T-A
• chr6-149413961-T-C
• chr6-149413961-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 0.557 in 152,048 control chromosomes in the GnomAD database, including 24,460 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 0.56 (24460 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84607 AN: 151930 Hom.: 24419 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.557 AC: 84713 AN: 152048 Hom.: 24460 Cov.: 32 AF XY: 0.557 AC XY: 41410 AN XY: 74324

African (AFR) AF: 0.706 AC: 29278 AN: 41494

American (AMR) AF: 0.557 AC: 8501 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1593 AN: 3472

East Asian (EAS) AF: 0.714 AC: 3684 AN: 5160

South Asian (SAS) AF: 0.485 AC: 2333 AN: 4810

European-Finnish (FIN) AF: 0.500 AC: 5284 AN: 10572

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32412 AN: 67962

Other (OTH) AF: 0.546 AC: 1152 AN: 2110

Alfa AF: 0.344 Hom.: 765

Bravo AF: 0.573

Asia WGS AF: 0.682 AC: 2366 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.18
DANN	Benign	0.72
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs366905; hg19: chr6-149735097;