rs7748777

Variant names:

• chr6-41166068-G-A
• rs7748777
• ENST00000702590.2:n.364+10505G>A

Variant summary

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

The ENST00000702590.2(ENSG00000290034):​n.364+10505G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 152,044 control chromosomes in the GnomAD database, including 28,131 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 0.58 (28131 hom., cov: 33)
• Consequence: ENSG00000290034 ENST00000702590.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 18 publications found

Genes affected

ENSG00000290034 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.86 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
ENSG00000290034	ENST00000702590.2	n.364+10505G>A		intron_variant	Intron 2 of 2
ENSG00000290034	ENST00000736037.1	n.364+10505G>A		intron_variant	Intron 2 of 2
ENSG00000290034	ENST00000736038.1	n.362+10507G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88137 AN: 151928 Hom.: 28074 Cov.: 33

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.580 AC: 88247 AN: 152044 Hom.: 28131 Cov.: 33 AF XY: 0.575 AC XY: 42716 AN XY: 74314

African (AFR) AF: 0.868 AC: 36022 AN: 41508

American (AMR) AF: 0.541 AC: 8270 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1702 AN: 3470

East Asian (EAS) AF: 0.401 AC: 2074 AN: 5172

South Asian (SAS) AF: 0.523 AC: 2523 AN: 4820

European-Finnish (FIN) AF: 0.413 AC: 4352 AN: 10530

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.465 AC: 31592 AN: 67946

Other (OTH) AF: 0.560 AC: 1182 AN: 2112

Alfa AF: 0.491 Hom.: 36948

Bravo AF: 0.601

Asia WGS AF: 0.557 AC: 1933 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.39
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7748777; hg19: chr6-41133806;