rs311408

Variant names:

• chr8-54201804-T-C
• rs311408
• ENST00000728273.1:n.205-6049T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-54201804-T-C
• chr8-54201804-T-G

Variant summary

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

The ENST00000728273.1(ENSG00000295151):​n.205-6049T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 151,794 control chromosomes in the GnomAD database, including 37,939 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 0.70 (37939 hom., cov: 30)
• Consequence: ENSG00000295151 ENST00000728273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 1 publications found

Genes affected

ENSG00000295151 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 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
ENSG00000295151	ENST00000728273.1	n.205-6049T>C		intron_variant	Intron 2 of 2
ENSG00000295151	ENST00000728274.1	n.87-6049T>C		intron_variant	Intron 1 of 1
ENSG00000295151	ENST00000728275.1	n.243-6049T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105544 AN: 151674 Hom.: 37902 Cov.: 30

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.696 AC: 105636 AN: 151794 Hom.: 37939 Cov.: 30 AF XY: 0.691 AC XY: 51178 AN XY: 74096

African (AFR) AF: 0.877 AC: 36366 AN: 41452

American (AMR) AF: 0.547 AC: 8326 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2288 AN: 3472

East Asian (EAS) AF: 0.583 AC: 2989 AN: 5130

South Asian (SAS) AF: 0.520 AC: 2487 AN: 4784

European-Finnish (FIN) AF: 0.666 AC: 6983 AN: 10490

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43898 AN: 67928

Other (OTH) AF: 0.689 AC: 1447 AN: 2100

Alfa AF: 0.680 Hom.: 4441

Bravo AF: 0.697

Asia WGS AF: 0.543 AC: 1890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.55
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs311408; hg19: chr8-55114364; COSMIC: COSV69028591;