6-86451173-C-T

Variant names:

• chr6-86451173-C-T
• rs3913972

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 0.288 in 152,112 control chromosomes in the GnomAD database, including 7,667 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 0.29 (7667 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 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: 0.289 AC: 43867 AN: 151994 Hom.: 7666 Cov.: 33

Gnomad AFR AF: 0.0863

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.288 AC: 43867 AN: 152112 Hom.: 7667 Cov.: 33 AF XY: 0.291 AC XY: 21662 AN XY: 74348

African (AFR) AF: 0.0861 AC: 3578 AN: 41542

American (AMR) AF: 0.338 AC: 5155 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1145 AN: 3472

East Asian (EAS) AF: 0.500 AC: 2581 AN: 5164

South Asian (SAS) AF: 0.333 AC: 1601 AN: 4814

European-Finnish (FIN) AF: 0.354 AC: 3736 AN: 10568

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25172 AN: 67962

Other (OTH) AF: 0.304 AC: 644 AN: 2116

Alfa AF: 0.231 Hom.: 806

Bravo AF: 0.280

Asia WGS AF: 0.370 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.66
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs3913972; hg19: chr6-87160891;