rs1323070

Variant names:

• chr6-75213889-A-G
• rs1323070

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 0.252 in 152,128 control chromosomes in the GnomAD database, including 6,066 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 0.25 (6066 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.471 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: 0.252 AC: 38319 AN: 152010 Hom.: 6054 Cov.: 33

Gnomad AFR AF: 0.0594

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.252 AC: 38338 AN: 152128 Hom.: 6066 Cov.: 33 AF XY: 0.257 AC XY: 19119 AN XY: 74344

African (AFR) AF: 0.0592 AC: 2461 AN: 41544

American (AMR) AF: 0.339 AC: 5181 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1221 AN: 3464

East Asian (EAS) AF: 0.487 AC: 2512 AN: 5160

South Asian (SAS) AF: 0.321 AC: 1549 AN: 4820

European-Finnish (FIN) AF: 0.349 AC: 3676 AN: 10544

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20802 AN: 67980

Other (OTH) AF: 0.268 AC: 567 AN: 2112

Alfa AF: 0.302 Hom.: 8524

Bravo AF: 0.247

Asia WGS AF: 0.393 AC: 1364 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	1.5
DANN	Benign	0.52
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs1323070; hg19: chr6-75923605; COSMIC: COSV69405509;