rs7001277

Variant names:

• chr8-73053924-A-G
• rs7001277
• ENST00000517664.1:n.1747A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-73053924-A-G
• chr8-73053924-A-T

Variant summary

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

The ENST00000517664.1(ENSG00000253636):​n.1747A>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 0.572 in 152,098 control chromosomes in the GnomAD database, including 26,427 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 0.57 (26427 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000253636 ENST00000517664.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488
• Publications: 3 publications found

Genes affected

ENSG00000253636 (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 (NFE) allele frequency at 95% confidence interval = 0.688 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
ENSG00000253636	ENST00000517664.1	n.1747A>G		non_coding_transcript_exon_variant	Exon 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87015 AN: 151980 Hom.: 26433 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.601

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.572 AC: 87048 AN: 152098 Hom.: 26427 Cov.: 32 AF XY: 0.569 AC XY: 42283 AN XY: 74352

African (AFR) AF: 0.400 AC: 16615 AN: 41500

American (AMR) AF: 0.489 AC: 7472 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2414 AN: 3468

East Asian (EAS) AF: 0.299 AC: 1545 AN: 5174

South Asian (SAS) AF: 0.593 AC: 2860 AN: 4820

European-Finnish (FIN) AF: 0.670 AC: 7081 AN: 10574

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47098 AN: 67978

Other (OTH) AF: 0.600 AC: 1264 AN: 2106

Alfa AF: 0.583 Hom.: 5401

Bravo AF: 0.550

Asia WGS AF: 0.465 AC: 1616 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.89
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs7001277; hg19: chr8-73966159;