chr6-153967448-G-A

Variant names:

• chr6-153967448-G-A
• rs11966947

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 0.271 in 152,020 control chromosomes in the GnomAD database, including 5,906 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 0.27 (5906 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.399 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: 0.271 AC: 41097 AN: 151902 Hom.: 5892 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.271 AC: 41124 AN: 152020 Hom.: 5906 Cov.: 32 AF XY: 0.279 AC XY: 20730 AN XY: 74322

African (AFR) AF: 0.324 AC: 13423 AN: 41448

American (AMR) AF: 0.407 AC: 6208 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 879 AN: 3470

East Asian (EAS) AF: 0.335 AC: 1735 AN: 5178

South Asian (SAS) AF: 0.389 AC: 1871 AN: 4814

European-Finnish (FIN) AF: 0.256 AC: 2702 AN: 10558

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13407 AN: 67980

Other (OTH) AF: 0.283 AC: 598 AN: 2112

Alfa AF: 0.118 Hom.: 191

Bravo AF: 0.278

Asia WGS AF: 0.395 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.47
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs11966947; hg19: chr6-154288583; COSMIC: COSV69027644;