rs6591348

Variant names:

• chr11-68673729-C-T
• rs6591348

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 0.167 in 152,188 control chromosomes in the GnomAD database, including 3,678 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 0.17 (3678 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.680
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 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: 0.167 AC: 25359 AN: 152072 Hom.: 3664 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0983

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0229

Gnomad SAS AF: 0.0664

Gnomad FIN AF: 0.0295

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.0878

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.167 AC: 25413 AN: 152188 Hom.: 3678 Cov.: 32 AF XY: 0.161 AC XY: 11954 AN XY: 74408

African (AFR) AF: 0.394 AC: 16330 AN: 41466

American (AMR) AF: 0.0981 AC: 1501 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3472

East Asian (EAS) AF: 0.0229 AC: 119 AN: 5188

South Asian (SAS) AF: 0.0659 AC: 318 AN: 4828

European-Finnish (FIN) AF: 0.0295 AC: 313 AN: 10614

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.0878 AC: 5974 AN: 68008

Other (OTH) AF: 0.148 AC: 313 AN: 2112

Alfa AF: 0.110 Hom.: 2280

Bravo AF: 0.181

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.9
DANN	Benign	0.44
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs6591348; hg19: chr11-68441197;