rs614565

Variant names:

• chr6-83732207-T-C
• rs614565
• ENST00000443471.3:n.709+4056T>C

Variant summary

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

The ENST00000443471.3(ENSG00000237874):​n.709+4056T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,088 control chromosomes in the GnomAD database, including 7,791 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 0.28 (7791 hom., cov: 32)
• Consequence: ENSG00000237874 ENST00000443471.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754
• Publications: 2 publications found

Genes affected

ENSG00000237874 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 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
ENSG00000237874	ENST00000443471.3	n.709+4056T>C		intron_variant	Intron 5 of 5	3
ENSG00000237874	ENST00000781263.1	n.290-4065T>C		intron_variant	Intron 1 of 1
ENSG00000237874	ENST00000781264.1	n.254-4091T>C		intron_variant	Intron 1 of 1
ENSG00000237874	ENST00000781265.1	n.375-4065T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42395 AN: 151972 Hom.: 7773 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.279 AC: 42455 AN: 152088 Hom.: 7791 Cov.: 32 AF XY: 0.275 AC XY: 20418 AN XY: 74366

African (AFR) AF: 0.522 AC: 21645 AN: 41436

American (AMR) AF: 0.207 AC: 3154 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 814 AN: 3472

East Asian (EAS) AF: 0.265 AC: 1374 AN: 5178

South Asian (SAS) AF: 0.283 AC: 1363 AN: 4808

European-Finnish (FIN) AF: 0.106 AC: 1120 AN: 10604

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12185 AN: 68008

Other (OTH) AF: 0.283 AC: 597 AN: 2112

Alfa AF: 0.263 Hom.: 1264

Bravo AF: 0.295

Asia WGS AF: 0.315 AC: 1097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.50
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs614565; hg19: chr6-84441926;