5-69166129-T-C

Variant names:

• chr5-69166129-T-C
• rs350099
• ENST00000690195.3:n.219A>G

Variant summary

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

The ENST00000690195.3(ENSG00000248664):​n.219A>G 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 0.434 in 151,958 control chromosomes in the GnomAD database, including 14,355 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 0.43 (14355 hom., cov: 31)
• Consequence: ENSG00000248664 ENST00000690195.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.605
• Publications: 6 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.537 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	ENST00000690195.3	n.219A>G		non_coding_transcript_exon_variant	Exon 2 of 6
ENSG00000248664	ENST00000777886.1	n.226A>G		non_coding_transcript_exon_variant	Exon 2 of 6
ENSG00000248664	ENST00000777887.1	n.217A>G		non_coding_transcript_exon_variant	Exon 2 of 7

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65880 AN: 151840 Hom.: 14341 Cov.: 31

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.434 AC: 65926 AN: 151958 Hom.: 14355 Cov.: 31 AF XY: 0.436 AC XY: 32360 AN XY: 74272

African (AFR) AF: 0.458 AC: 18974 AN: 41420

American (AMR) AF: 0.453 AC: 6914 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1274 AN: 3470

East Asian (EAS) AF: 0.458 AC: 2358 AN: 5148

South Asian (SAS) AF: 0.555 AC: 2669 AN: 4812

European-Finnish (FIN) AF: 0.387 AC: 4087 AN: 10564

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28045 AN: 67964

Other (OTH) AF: 0.420 AC: 887 AN: 2112

Alfa AF: 0.416 Hom.: 2764

Bravo AF: 0.436

Asia WGS AF: 0.523 AC: 1817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.6
DANN	Benign	0.85
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs350099; hg19: chr5-68461956; COSMIC: COSV56509405;