chr6-78225040-G-C

Variant names:

• chr6-78225040-G-C
• rs3857446
• ENST00000715178.1:n.1038-21087C>G

Variant summary

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

The ENST00000715178.1(ENSG00000230309):​n.1038-21087C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 150,552 control chromosomes in the GnomAD database, including 4,180 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 0.22 (4180 hom., cov: 31)
• Consequence: ENSG00000230309 ENST00000715178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 4 publications found

Genes affected

ENSG00000230309 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377865	XR_002956359.2	n.135-21087C>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230309	ENST00000715178.1	n.1038-21087C>G		intron_variant	Intron 6 of 14

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32549 AN: 150454 Hom.: 4178 Cov.: 31

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.100

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.216 AC: 32571 AN: 150552 Hom.: 4180 Cov.: 31 AF XY: 0.221 AC XY: 16239 AN XY: 73504

African (AFR) AF: 0.299 AC: 12174 AN: 40744

American (AMR) AF: 0.297 AC: 4505 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 810 AN: 3442

East Asian (EAS) AF: 0.495 AC: 2498 AN: 5048

South Asian (SAS) AF: 0.180 AC: 862 AN: 4802

European-Finnish (FIN) AF: 0.165 AC: 1732 AN: 10480

Middle Eastern (MID) AF: 0.0972 AC: 28 AN: 288

European-Non Finnish (NFE) AF: 0.138 AC: 9338 AN: 67592

Other (OTH) AF: 0.210 AC: 438 AN: 2086

Alfa AF: 0.0741 Hom.: 82

Bravo AF: 0.234

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.44
DANN	Benign	0.64
PhyloP100		0.013

Splicing

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

Other links and lift over

dbSNP: rs3857446; hg19: chr6-78934757;