6-94521445-G-C

Variant names:

• chr6-94521445-G-C
• rs222541

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 0.489 in 151,520 control chromosomes in the GnomAD database, including 22,110 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 0.49 (22110 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 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: 0.488 AC: 73938 AN: 151402 Hom.: 22052 Cov.: 32

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.489 AC: 74037 AN: 151520 Hom.: 22110 Cov.: 32 AF XY: 0.489 AC XY: 36206 AN XY: 74054

African (AFR) AF: 0.844 AC: 34965 AN: 41420

American (AMR) AF: 0.321 AC: 4873 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1510 AN: 3460

East Asian (EAS) AF: 0.567 AC: 2909 AN: 5134

South Asian (SAS) AF: 0.535 AC: 2581 AN: 4820

European-Finnish (FIN) AF: 0.318 AC: 3354 AN: 10554

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.330 AC: 22321 AN: 67658

Other (OTH) AF: 0.454 AC: 953 AN: 2100

Alfa AF: 0.278 Hom.: 775

Bravo AF: 0.502

Asia WGS AF: 0.588 AC: 2044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.68
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs222541; hg19: chr6-95231163;