rs72624931

Variant names:

• chr7-128410394-G-A
• rs72624931
• ENST00000784862.1:n.470C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000784862.1(ENSG00000302195):​n.470C>T 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 0.0178 in 152,804 control chromosomes in the GnomAD database, including 41 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 0.018 (41 hom., cov: 33)
  • Exomes 𝑓: 0.023 (0 hom.)
• Consequence: ENSG00000302195 ENST00000784862.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 1 publications found

Genes affected

ENSG00000302195 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0178 (2713/152364) while in subpopulation SAS AF = 0.0547 (264/4828). AF 95% confidence interval is 0.0493. There are 41 homozygotes in GnomAd4. There are 1333 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 41 gene

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
ENSG00000302195	ENST00000784862.1	n.470C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0178 AC: 2715 AN: 152246 Hom.: 41 Cov.: 33

Gnomad AFR AF: 0.00610

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0196

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0550

Gnomad FIN AF: 0.00659

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0249

Gnomad OTH AF: 0.0206

GnomAD4 exome AF: 0.0227 AC: 10 AN: 440 Hom.: 0 AF XY: 0.0248 AC XY: 6 AN XY: 242

African (AFR) AF: 0.00 AC: 0 AN: 22

American (AMR) AF: 0.00 AC: 0 AN: 12

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20

East Asian (EAS) AF: 0.00 AC: 0 AN: 12

South Asian (SAS) AF: 0.0417 AC: 1 AN: 24

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0267 AC: 8 AN: 300

Other (OTH) AF: 0.0263 AC: 1 AN: 38

GnomAD4 genome AF: 0.0178 AC: 2713 AN: 152364 Hom.: 41 Cov.: 33 AF XY: 0.0179 AC XY: 1333 AN XY: 74504

African (AFR) AF: 0.00608 AC: 253 AN: 41592

American (AMR) AF: 0.0196 AC: 300 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0193 AC: 67 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.0547 AC: 264 AN: 4828

European-Finnish (FIN) AF: 0.00659 AC: 70 AN: 10628

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0249 AC: 1697 AN: 68032

Other (OTH) AF: 0.0203 AC: 43 AN: 2114

Alfa AF: 0.0185 Hom.: 5

Bravo AF: 0.0170

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.5
DANN	Benign	0.92
PhyloP100		-1.7
PromoterAI		-0.044	Neutral

Splicing

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

Other links and lift over

dbSNP: rs72624931; hg19: chr7-128050448;