chr5-111091649-G-A

Variant names:

• chr5-111091649-G-A
• rs7723819
• ENST00000507269.3:n.46+421C>T

Variant summary

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

The ENST00000507269.3(ENSG00000253613):​n.46+421C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 153,656 control chromosomes in the GnomAD database, including 22,483 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 0.53 (22255 hom., cov: 32)
  • Exomes 𝑓: 0.50 (228 hom.)
• Consequence: ENSG00000253613 ENST00000507269.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• Publications: 23 publications found

Genes affected

ENSG00000253613 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507269.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253613	ENST00000507269.3	TSL:5	n.46+421C>T		intron	N/A
	ENSG00000253613	ENST00000741219.1		n.136+421C>T		intron	N/A
	ENSG00000253613	ENST00000741220.1		n.136+421C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80809 AN: 151906 Hom.: 22228 Cov.: 32

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.522

GnomAD4 exome AF: 0.504 AC: 822 AN: 1632 Hom.: 228 AF XY: 0.543 AC XY: 456 AN XY: 840

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 0.618 AC: 183 AN: 296

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.423 AC: 11 AN: 26

South Asian (SAS) AF: 0.741 AC: 83 AN: 112

European-Finnish (FIN) AF: 0.667 AC: 4 AN: 6

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.451 AC: 513 AN: 1138

Other (OTH) AF: 0.480 AC: 24 AN: 50

GnomAD4 genome AF: 0.532 AC: 80891 AN: 152024 Hom.: 22255 Cov.: 32 AF XY: 0.538 AC XY: 39990 AN XY: 74314

African (AFR) AF: 0.657 AC: 27233 AN: 41470

American (AMR) AF: 0.542 AC: 8287 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1663 AN: 3472

East Asian (EAS) AF: 0.397 AC: 2041 AN: 5138

South Asian (SAS) AF: 0.681 AC: 3278 AN: 4816

European-Finnish (FIN) AF: 0.548 AC: 5794 AN: 10582

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30998 AN: 67956

Other (OTH) AF: 0.521 AC: 1099 AN: 2110

Alfa AF: 0.481 Hom.: 59769

Bravo AF: 0.530

Asia WGS AF: 0.534 AC: 1861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.2
DANN	Benign	0.78
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs7723819; hg19: chr5-110427347;