rs1341242

Variant names:

• chr6-17299599-T-G
• rs1341242

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 0.641 in 151,908 control chromosomes in the GnomAD database, including 31,942 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 0.64 (31942 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 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: 0.641 AC: 97359 AN: 151790 Hom.: 31909 Cov.: 31

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.641 AC: 97446 AN: 151908 Hom.: 31942 Cov.: 31 AF XY: 0.634 AC XY: 47079 AN XY: 74240

African (AFR) AF: 0.780 AC: 32306 AN: 41416

American (AMR) AF: 0.575 AC: 8778 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2157 AN: 3470

East Asian (EAS) AF: 0.606 AC: 3111 AN: 5136

South Asian (SAS) AF: 0.524 AC: 2515 AN: 4796

European-Finnish (FIN) AF: 0.561 AC: 5908 AN: 10536

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40505 AN: 67970

Other (OTH) AF: 0.646 AC: 1363 AN: 2110

Alfa AF: 0.609 Hom.: 3705

Bravo AF: 0.653

Asia WGS AF: 0.607 AC: 2107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.48
DANN	Benign	0.60
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1341242; hg19: chr6-17299830;