rs5992507

Variant names:

• chr22-20069935-A-G
• rs5992507
• ENST00000595864.5:n.291+36T>C

Variant summary

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

The ENST00000595864.5(ENSG00000236540):​n.291+36T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,312 control chromosomes in the GnomAD database, including 2,177 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 0.13 (2176 hom., cov: 33)
  • Exomes 𝑓: 0.17 (1 hom.)
• Consequence: ENSG00000236540 ENST00000595864.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 5 publications found

Genes affected

ENSG00000236540 (HGNC:41096):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 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
ENSG00000236540	ENST00000595864.5	n.291+36T>C		intron_variant	Intron 1 of 3	5
ENSG00000236540	ENST00000596334.5	n.599+36T>C		intron_variant	Intron 1 of 3	5
ENSG00000236540	ENST00000598339.5	n.552+36T>C		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20270 AN: 152116 Hom.: 2168 Cov.: 33

Gnomad AFR AF: 0.0453

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.0823

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.131

GnomAD4 exome AF: 0.167 AC: 13 AN: 78 Hom.: 1 Cov.: 0 AF XY: 0.161 AC XY: 10 AN XY: 62

African (AFR) AF: 0.00 AC: 0 AN: 2

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) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.177 AC: 11 AN: 62

Other (OTH) AF: 0.100 AC: 1 AN: 10

GnomAD4 genome AF: 0.133 AC: 20297 AN: 152234 Hom.: 2176 Cov.: 33 AF XY: 0.141 AC XY: 10529 AN XY: 74420

African (AFR) AF: 0.0453 AC: 1885 AN: 41570

American (AMR) AF: 0.266 AC: 4077 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0823 AC: 285 AN: 3464

East Asian (EAS) AF: 0.480 AC: 2481 AN: 5166

South Asian (SAS) AF: 0.208 AC: 1005 AN: 4828

European-Finnish (FIN) AF: 0.150 AC: 1595 AN: 10598

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8578 AN: 67988

Other (OTH) AF: 0.135 AC: 285 AN: 2112

Alfa AF: 0.130 Hom.: 824

Bravo AF: 0.140

Asia WGS AF: 0.292 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.14
DANN	Benign	0.81
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs5992507; hg19: chr22-20057458;