chr6-65883272-T-C

Variant names:

• chr6-65883272-T-C
• rs1938115
• ENST00000800215.1:n.218+17681A>G

Variant summary

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

The ENST00000800215.1(ENSG00000304165):​n.218+17681A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 152,024 control chromosomes in the GnomAD database, including 23,655 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 0.55 (23655 hom., cov: 33)
• Consequence: ENSG00000304165 ENST00000800215.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 2 publications found

Genes affected

ENSG00000304165 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000800215.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304165	ENST00000800215.1		n.218+17681A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84258 AN: 151906 Hom.: 23623 Cov.: 33

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.555 AC: 84347 AN: 152024 Hom.: 23655 Cov.: 33 AF XY: 0.565 AC XY: 41996 AN XY: 74306

African (AFR) AF: 0.529 AC: 21940 AN: 41474

American (AMR) AF: 0.623 AC: 9494 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1781 AN: 3468

East Asian (EAS) AF: 0.779 AC: 4022 AN: 5164

South Asian (SAS) AF: 0.665 AC: 3208 AN: 4822

European-Finnish (FIN) AF: 0.587 AC: 6204 AN: 10562

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35926 AN: 67970

Other (OTH) AF: 0.564 AC: 1191 AN: 2112

Alfa AF: 0.547 Hom.: 3011

Bravo AF: 0.556

Asia WGS AF: 0.715 AC: 2484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.38
DANN	Benign	0.77
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1938115; hg19: chr6-66593165;