chr6-8349278-T-C

Variant names:

• chr6-8349278-T-C
• rs2185503
• ENST00000644718.1:n.560+41718T>C

Variant summary

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

The ENST00000644718.1(ENSG00000285216):​n.560+41718T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,076 control chromosomes in the GnomAD database, including 10,052 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 0.35 (10052 hom., cov: 32)
• Consequence: ENSG00000285216 ENST00000644718.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 3 publications found

Genes affected

ENSG00000285216 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644718.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285216	ENST00000644718.1		n.560+41718T>C		intron	N/A
	ENSG00000234763	ENST00000651914.1		n.312-6630A>G		intron	N/A
	ENSG00000234763	ENST00000655767.2		n.375-6630A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52881 AN: 151958 Hom.: 10038 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.348 AC: 52927 AN: 152076 Hom.: 10052 Cov.: 32 AF XY: 0.339 AC XY: 25221 AN XY: 74348

African (AFR) AF: 0.496 AC: 20563 AN: 41444

American (AMR) AF: 0.276 AC: 4221 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1334 AN: 3470

East Asian (EAS) AF: 0.157 AC: 809 AN: 5166

South Asian (SAS) AF: 0.338 AC: 1629 AN: 4816

European-Finnish (FIN) AF: 0.205 AC: 2177 AN: 10596

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 20989 AN: 67990

Other (OTH) AF: 0.381 AC: 806 AN: 2116

Alfa AF: 0.323 Hom.: 35066

Bravo AF: 0.360

Asia WGS AF: 0.255 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.76
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs2185503; hg19: chr6-8349511;