chr6-31605150-T-C

Variant names:

• chr6-31605150-T-C
• rs9378200

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 0.0593 in 151,008 control chromosomes in the GnomAD database, including 490 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 0.059 (490 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.416
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 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: 0.0594 AC: 8963 AN: 150894 Hom.: 490 Cov.: 30

Gnomad AFR AF: 0.0123

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0457

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0370

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0648

Gnomad OTH AF: 0.0564

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

GnomAD4 genome AF: 0.0593 AC: 8960 AN: 151008 Hom.: 490 Cov.: 30 AF XY: 0.0622 AC XY: 4587 AN XY: 73708

African (AFR) AF: 0.0123 AC: 506 AN: 41056

American (AMR) AF: 0.0458 AC: 692 AN: 15108

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 416 AN: 3464

East Asian (EAS) AF: 0.266 AC: 1360 AN: 5104

South Asian (SAS) AF: 0.191 AC: 917 AN: 4794

European-Finnish (FIN) AF: 0.0370 AC: 382 AN: 10326

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0647 AC: 4393 AN: 67854

Other (OTH) AF: 0.0577 AC: 121 AN: 2098

Alfa AF: 0.0636 Hom.: 1297

Bravo AF: 0.0544

Asia WGS AF: 0.155 AC: 536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	15
DANN	Benign	0.91
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs9378200; hg19: chr6-31572927;