chr6-30119999-G-C

Variant names:

• chr6-30119999-G-C
• rs9261434

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 0.916 in 152,258 control chromosomes in the GnomAD database, including 64,023 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 0.92 (64023 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 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: 0.916 AC: 139320 AN: 152140 Hom.: 63955 Cov.: 31

Gnomad AFR AF: 0.967

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.935

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.942

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.916 AC: 139447 AN: 152258 Hom.: 64023 Cov.: 31 AF XY: 0.916 AC XY: 68199 AN XY: 74442

African (AFR) AF: 0.967 AC: 40191 AN: 41550

American (AMR) AF: 0.935 AC: 14314 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.927 AC: 3219 AN: 3472

East Asian (EAS) AF: 0.988 AC: 5116 AN: 5178

South Asian (SAS) AF: 0.943 AC: 4550 AN: 4826

European-Finnish (FIN) AF: 0.884 AC: 9366 AN: 10600

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.877 AC: 59620 AN: 68014

Other (OTH) AF: 0.918 AC: 1935 AN: 2108

Alfa AF: 0.853 Hom.: 3146

Bravo AF: 0.924

Asia WGS AF: 0.964 AC: 3355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.081
DANN	Benign	0.43
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs9261434; hg19: chr6-30087776;