rs222541

Positions:

• chr6-94521445-G-C
• chr6-94521445-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.454

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs222541; hg19: chr6-95231163;