rs1321355

Variant names:

• chr6-89241194-A-G
• rs1321355

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.344 in 152,152 control chromosomes in the GnomAD database, including 10,618 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 (10618 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 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: 0.344 AC: 52327 AN: 152034 Hom.: 10598 Cov.: 33

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.344 AC: 52390 AN: 152152 Hom.: 10618 Cov.: 33 AF XY: 0.338 AC XY: 25146 AN XY: 74382

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.0774

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.287

Alfa AF: 0.296 Hom.: 3803

Bravo AF: 0.346

Asia WGS AF: 0.218 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.20
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1321355; hg19: chr6-89950913; COSMIC: COSV69412405;