rs6835457

Variant names:

• chr4-122589971-A-G
• rs6835457
• ENST00000776599.1:n.593T>C

Variant summary

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

The ENST00000776599.1(ENSG00000301148):​n.593T>C 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 0.348 in 152,090 control chromosomes in the GnomAD database, including 9,587 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 0.35 (9587 hom., cov: 32)
• Consequence: ENSG00000301148 ENST00000776599.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.601
• Publications: 6 publications found

Genes affected

ENSG00000301148 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 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
ENSG00000301148	ENST00000776599.1	n.593T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52908 AN: 151970 Hom.: 9577 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.348 AC: 52957 AN: 152090 Hom.: 9587 Cov.: 32 AF XY: 0.342 AC XY: 25428 AN XY: 74356

African (AFR) AF: 0.401 AC: 16615 AN: 41480

American (AMR) AF: 0.372 AC: 5677 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1185 AN: 3472

East Asian (EAS) AF: 0.458 AC: 2363 AN: 5158

South Asian (SAS) AF: 0.295 AC: 1419 AN: 4812

European-Finnish (FIN) AF: 0.198 AC: 2095 AN: 10598

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22468 AN: 67974

Other (OTH) AF: 0.333 AC: 704 AN: 2112

Alfa AF: 0.324 Hom.: 1109

Bravo AF: 0.366

Asia WGS AF: 0.369 AC: 1282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.49
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs6835457; hg19: chr4-123511126;