rs7224260

Variant names:

• chr17-40012360-C-T
• rs7224260
• ENST00000583462.1:n.650G>A

Variant summary

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

The ENST00000583462.1(ENSG00000265799):​n.650G>A 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 0.153 in 152,216 control chromosomes in the GnomAD database, including 1,981 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 0.15 (1980 hom., cov: 32)
  • Exomes 𝑓: 0.13 (1 hom.)
• Consequence: ENSG00000265799 ENST00000583462.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 7 publications found

Genes affected

ENSG00000265799 (HGNC:58140):

ENSG00000304239 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSMD3-AS1	NR_198981.1	n.655G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000265799	ENST00000583462.1	n.650G>A		non_coding_transcript_exon_variant	Exon 2 of 2	3
ENSG00000304239	ENST00000801359.1	n.20C>T		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000265799	ENST00000801108.1	n.537+202G>A		intron_variant	Intron 2 of 3
ENSG00000265799	ENST00000584649.1	n.*184G>A		downstream_gene_variant		4

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23279 AN: 152046 Hom.: 1980 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00597

Gnomad SAS AF: 0.0674

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.144

GnomAD4 exome AF: 0.135 AC: 7 AN: 52 Hom.: 1 Cov.: 0 AF XY: 0.0750 AC XY: 3 AN XY: 40

African (AFR) AF: 0.333 AC: 2 AN: 6

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.119 AC: 5 AN: 42

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.153 AC: 23284 AN: 152164 Hom.: 1980 Cov.: 32 AF XY: 0.149 AC XY: 11090 AN XY: 74384

African (AFR) AF: 0.183 AC: 7604 AN: 41504

American (AMR) AF: 0.121 AC: 1842 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 392 AN: 3472

East Asian (EAS) AF: 0.00599 AC: 31 AN: 5178

South Asian (SAS) AF: 0.0681 AC: 328 AN: 4818

European-Finnish (FIN) AF: 0.148 AC: 1564 AN: 10598

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.163 AC: 11081 AN: 67992

Other (OTH) AF: 0.143 AC: 302 AN: 2114

Alfa AF: 0.154 Hom.: 682

Bravo AF: 0.153

Asia WGS AF: 0.0620 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.34
DANN	Benign	0.48
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7224260; hg19: chr17-38168613;