rs7553007

Variant names:

• chr1-159728759-G-A
• rs7553007
• ENST00000751816.1:n.244+2096G>A

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.244+2096G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,952 control chromosomes in the GnomAD database, including 8,117 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 0.32 (8117 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 54 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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
ENSG00000297913	ENST00000751816.1	n.244+2096G>A		intron_variant	Intron 2 of 2
ENSG00000297913	ENST00000751817.1	n.356+1585G>A		intron_variant	Intron 3 of 3
ENSG00000297913	ENST00000751818.1	n.199+2096G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48297 AN: 151834 Hom.: 8110 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.318 AC: 48323 AN: 151952 Hom.: 8117 Cov.: 32 AF XY: 0.322 AC XY: 23888 AN XY: 74244

African (AFR) AF: 0.226 AC: 9364 AN: 41440

American (AMR) AF: 0.372 AC: 5672 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1308 AN: 3472

East Asian (EAS) AF: 0.581 AC: 2992 AN: 5152

South Asian (SAS) AF: 0.304 AC: 1464 AN: 4814

European-Finnish (FIN) AF: 0.371 AC: 3915 AN: 10540

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22603 AN: 67956

Other (OTH) AF: 0.336 AC: 710 AN: 2110

Alfa AF: 0.335 Hom.: 38769

Bravo AF: 0.314

Asia WGS AF: 0.440 AC: 1531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.21
DANN	Benign	0.65
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7553007; hg19: chr1-159698549;