rs1323604

Variant names:

• chr13-42727070-A-G
• rs1323604
• ENST00000799325.1:n.356-6369T>C

Your query was ambiguous. Multiple possible variants found:

• chr13-42727070-A-G
• chr13-42727070-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000799325.1(ENSG00000304062):​n.356-6369T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.962 in 152,184 control chromosomes in the GnomAD database, including 70,639 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 0.96 (70639 hom., cov: 32)
• Consequence: ENSG00000304062 ENST00000799325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197
• Publications: 0 publications found

Genes affected

ENSG00000304062 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903164	XM_047430822.1	c.131-6369T>C		intron_variant	Intron 1 of 2		XP_047286778.1
LOC124903164	XR_007063769.1	n.671-6369T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304062	ENST00000799325.1	n.356-6369T>C		intron_variant	Intron 1 of 3
ENSG00000304062	ENST00000799326.1	n.762-6369T>C		intron_variant	Intron 2 of 3
ENSG00000304062	ENST00000799327.1	n.359-6369T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146302 AN: 152066 Hom.: 70600 Cov.: 32

Gnomad AFR AF: 0.872

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.984

Gnomad ASJ AF: 0.993

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.972

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

GnomAD4 genome AF: 0.962 AC: 146399 AN: 152184 Hom.: 70639 Cov.: 32 AF XY: 0.963 AC XY: 71654 AN XY: 74404

African (AFR) AF: 0.872 AC: 36184 AN: 41512

American (AMR) AF: 0.984 AC: 15011 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.993 AC: 3449 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5184 AN: 5184

South Asian (SAS) AF: 0.999 AC: 4818 AN: 4822

European-Finnish (FIN) AF: 1.00 AC: 10619 AN: 10622

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67891 AN: 68004

Other (OTH) AF: 0.972 AC: 2051 AN: 2110

Alfa AF: 0.980 Hom.: 18911

Bravo AF: 0.957

Asia WGS AF: 0.988 AC: 3428 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.46
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1323604; hg19: chr13-43301206;