6-100371358-A-T

Variant names:

• chr6-100371358-A-T
• rs1506083

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 0.26 in 151,960 control chromosomes in the GnomAD database, including 5,711 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 0.26 (5711 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.554 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: 0.260 AC: 39412 AN: 151842 Hom.: 5691 Cov.: 31

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.260 AC: 39465 AN: 151960 Hom.: 5711 Cov.: 31 AF XY: 0.263 AC XY: 19554 AN XY: 74266

African (AFR) AF: 0.152 AC: 6300 AN: 41458

American (AMR) AF: 0.334 AC: 5101 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 887 AN: 3472

East Asian (EAS) AF: 0.571 AC: 2941 AN: 5148

South Asian (SAS) AF: 0.251 AC: 1211 AN: 4828

European-Finnish (FIN) AF: 0.292 AC: 3079 AN: 10548

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.282 AC: 19129 AN: 67922

Other (OTH) AF: 0.262 AC: 553 AN: 2112

Alfa AF: 0.273 Hom.: 722

Bravo AF: 0.260

Asia WGS AF: 0.390 AC: 1353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.39
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1506083; hg19: chr6-100819234;