rs1324072

Variant names:

• chr6-88113218-C-G
• rs1324072

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 0.138 in 152,206 control chromosomes in the GnomAD database, including 1,555 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 0.14 (1555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 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: 0.138 AC: 21003 AN: 152088 Hom.: 1545 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0499

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.138 AC: 21047 AN: 152206 Hom.: 1555 Cov.: 32 AF XY: 0.139 AC XY: 10332 AN XY: 74432

African (AFR) AF: 0.121 AC: 5025 AN: 41548

American (AMR) AF: 0.111 AC: 1690 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3470

East Asian (EAS) AF: 0.0498 AC: 258 AN: 5182

South Asian (SAS) AF: 0.194 AC: 935 AN: 4820

European-Finnish (FIN) AF: 0.156 AC: 1656 AN: 10596

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10760 AN: 67988

Other (OTH) AF: 0.151 AC: 318 AN: 2110

Alfa AF: 0.151 Hom.: 212

Bravo AF: 0.132

Asia WGS AF: 0.148 AC: 515 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.9
DANN	Benign	0.41
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs1324072; hg19: chr6-88822936;