5-69166611-C-T

Variant names:

• chr5-69166611-C-T
• rs350104
• ENST00000777908.1:n.321G>A

Variant summary

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

The ENST00000777908.1(ENSG00000248664):​n.321G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 150,920 control chromosomes in the GnomAD database, including 29,734 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 0.62 (29734 hom., cov: 27)
• Consequence: ENSG00000248664 ENST00000777908.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547
• Publications: 12 publications found

Genes affected

ENSG00000248664 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 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
ENSG00000248664	ENST00000777908.1	n.321G>A		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000248664	ENST00000690195.3	n.81+260G>A		intron_variant	Intron 1 of 5
ENSG00000248664	ENST00000777886.1	n.88+260G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.619 AC: 93314 AN: 150808 Hom.: 29684 Cov.: 27

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.619 AC: 93425 AN: 150920 Hom.: 29734 Cov.: 27 AF XY: 0.624 AC XY: 45892 AN XY: 73580

African (AFR) AF: 0.767 AC: 31470 AN: 41050

American (AMR) AF: 0.641 AC: 9734 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1814 AN: 3464

East Asian (EAS) AF: 0.699 AC: 3578 AN: 5118

South Asian (SAS) AF: 0.675 AC: 3229 AN: 4782

European-Finnish (FIN) AF: 0.566 AC: 5790 AN: 10224

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.528 AC: 35778 AN: 67814

Other (OTH) AF: 0.601 AC: 1258 AN: 2092

Alfa AF: 0.590 Hom.: 4088

Bravo AF: 0.627

Asia WGS AF: 0.700 AC: 2437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.9
DANN	Benign	0.80
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs350104; hg19: chr5-68462438;