rs4948088

Variant names:

• chr7-50959497-A-C
• rs4948088
• ENST00000758591.1:n.78A>C

Your query was ambiguous. Multiple possible variants found:

• chr7-50959497-A-C
• chr7-50959497-A-G
• chr7-50959497-A-T

Variant summary

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

The ENST00000758800.1(ENSG00000298899):​n.270+5T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.957 in 152,280 control chromosomes in the GnomAD database, including 69,701 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 0.96 (69701 hom., cov: 32)
• Consequence: ENSG00000298899 ENST00000758800.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.32
• Publications: 58 publications found

Genes affected

ENSG00000298883 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758800.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298883	ENST00000758591.1		n.78A>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000298899	ENST00000758799.1		n.485T>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000228204	ENST00000420449.1	TSL:5	n.25-57896A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.957 AC: 145567 AN: 152162 Hom.: 69651 Cov.: 32

Gnomad AFR AF: 0.949

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.981

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.967

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

GnomAD4 genome AF: 0.957 AC: 145673 AN: 152280 Hom.: 69701 Cov.: 32 AF XY: 0.958 AC XY: 71361 AN XY: 74458

African (AFR) AF: 0.949 AC: 39443 AN: 41546

American (AMR) AF: 0.937 AC: 14329 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.989 AC: 3433 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5154 AN: 5160

South Asian (SAS) AF: 0.962 AC: 4636 AN: 4818

European-Finnish (FIN) AF: 0.981 AC: 10417 AN: 10624

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.956 AC: 65019 AN: 68040

Other (OTH) AF: 0.967 AC: 2046 AN: 2116

Alfa AF: 0.958 Hom.: 206489

Bravo AF: 0.953

Asia WGS AF: 0.966 AC: 3361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.57
PhyloP100		-3.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4948088;

hg19: chr7-51027194;