rs1321742

Variant names:

• chr6-85171471-A-C
• rs1321742

Your query was ambiguous. Multiple possible variants found:

• chr6-85171471-A-C
• chr6-85171471-A-G
• chr6-85171471-A-T

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 0.345 in 152,096 control chromosomes in the GnomAD database, including 9,924 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 0.34 (9924 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 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: 0.345 AC: 52381 AN: 151978 Hom.: 9924 Cov.: 33

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.345 AC: 52415 AN: 152096 Hom.: 9924 Cov.: 33 AF XY: 0.350 AC XY: 26056 AN XY: 74370

African (AFR) AF: 0.425 AC: 17608 AN: 41476

American (AMR) AF: 0.489 AC: 7482 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1191 AN: 3466

East Asian (EAS) AF: 0.603 AC: 3123 AN: 5176

South Asian (SAS) AF: 0.404 AC: 1948 AN: 4820

European-Finnish (FIN) AF: 0.268 AC: 2835 AN: 10574

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.252 AC: 17134 AN: 67970

Other (OTH) AF: 0.354 AC: 746 AN: 2110

Alfa AF: 0.291 Hom.: 22261

Bravo AF: 0.365

Asia WGS AF: 0.506 AC: 1759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.7
DANN	Benign	0.53
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1321742; hg19: chr6-85881189;