rs538360

Variant names:

• chr6-81453804-C-G
• rs538360
• ENST00000759357.1:n.200-7744G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-81453804-C-G
• chr6-81453804-C-T

Variant summary

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

The ENST00000759357.1(ENSG00000298959):​n.200-7744G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.974 in 152,298 control chromosomes in the GnomAD database, including 72,234 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 0.97 (72234 hom., cov: 32)
• Consequence: ENSG00000298959 ENST00000759357.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.733
• Publications: 1 publications found

Genes affected

ENSG00000298959 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000759357.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298959	ENST00000759357.1		n.200-7744G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.974 AC: 148194 AN: 152180 Hom.: 72168 Cov.: 32

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 0.992

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.965

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.960

Gnomad OTH AF: 0.976

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

GnomAD4 genome AF: 0.974 AC: 148319 AN: 152298 Hom.: 72234 Cov.: 32 AF XY: 0.975 AC XY: 72554 AN XY: 74452

African (AFR) AF: 0.991 AC: 41209 AN: 41566

American (AMR) AF: 0.980 AC: 14987 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.992 AC: 3443 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5134 AN: 5164

South Asian (SAS) AF: 0.967 AC: 4669 AN: 4830

European-Finnish (FIN) AF: 0.973 AC: 10334 AN: 10622

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.960 AC: 65291 AN: 68032

Other (OTH) AF: 0.976 AC: 2064 AN: 2114

Alfa AF: 0.961 Hom.: 8191

Bravo AF: 0.976

Asia WGS AF: 0.981 AC: 3410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.3
DANN	Benign	0.42
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs538360; hg19: chr6-82163521;