rs6665519

Variant names:

• chr1-235903172-T-C
• rs6665519
• ENST00000786960.1:n.395T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-235903172-T-C
• chr1-235903172-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000786960.1(ENSG00000302457):​n.395T>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 0.0000133 in 150,030 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000013 (0 hom., cov: 24)
• Consequence: ENSG00000302457 ENST00000786960.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 4 publications found

Genes affected

ENSG00000302457 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373215	XR_001738543.2	n.534T>C		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105373215	XR_001738537.2	n.519+9942T>C		intron_variant	Intron 2 of 2
LOC105373215	XR_001738539.2	n.519+9942T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302457	ENST00000786960.1	n.395T>C		non_coding_transcript_exon_variant	Exon 4 of 5
ENSG00000302457	ENST00000786961.1	n.395T>C		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000302457	ENST00000786952.1	n.209+9942T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0000133 AC: 2 AN: 150030 Hom.: 0 Cov.: 24

Gnomad AFR AF: 0.0000493

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000133 AC: 2 AN: 150030 Hom.: 0 Cov.: 24 AF XY: 0.0000137 AC XY: 1 AN XY: 72956

African (AFR) AF: 0.0000493 AC: 2 AN: 40594

American (AMR) AF: 0.00 AC: 0 AN: 15022

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5112

South Asian (SAS) AF: 0.00 AC: 0 AN: 4670

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10118

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67756

Other (OTH) AF: 0.00 AC: 0 AN: 2070

Alfa AF: 0.00 Hom.: 6161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	13
DANN	Benign	0.64
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs6665519; hg19: chr1-236066472;