rs77693245

Variant names:

• chr6-84765153-G-A
• rs77693245
• ENST00000790820.1:n.185+2667G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-84765153-G-A
• chr6-84765153-G-C
• chr6-84765153-G-T

Variant summary

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

The ENST00000790820.1(ENSG00000287294):​n.185+2667G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0495 in 152,216 control chromosomes in the GnomAD database, including 223 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 0.050 (223 hom., cov: 33)
• Consequence: ENSG00000287294 ENST00000790820.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.842
• Publications: 1 publications found

Genes affected

ENSG00000287294 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0735 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000790820.1. 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
	ENSG00000287294	ENST00000790820.1		n.185+2667G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0495 AC: 7522 AN: 152098 Hom.: 223 Cov.: 33

Gnomad AFR AF: 0.0755

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.0454

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.0208

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0418

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0495 AC: 7538 AN: 152216 Hom.: 223 Cov.: 33 AF XY: 0.0480 AC XY: 3573 AN XY: 74424

African (AFR) AF: 0.0757 AC: 3144 AN: 41518

American (AMR) AF: 0.0453 AC: 693 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 154 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.0313 AC: 151 AN: 4824

European-Finnish (FIN) AF: 0.0208 AC: 220 AN: 10598

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0418 AC: 2844 AN: 68018

Other (OTH) AF: 0.0625 AC: 132 AN: 2112

Alfa AF: 0.0394 Hom.: 226

Bravo AF: 0.0527

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
DANN	Benign	0.74
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs77693245; hg19: chr6-85474871;