rs7722165

Variant names:

• chr5-173507967-C-A
• rs7722165
• ENST00000827042.1:n.446+1595C>A

Variant summary

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

The ENST00000827042.1(ENSG00000253968):​n.446+1595C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,010 control chromosomes in the GnomAD database, including 10,395 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 0.37 (10395 hom., cov: 32)
• Consequence: ENSG00000253968 ENST00000827042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.401
• Publications: 2 publications found

Genes affected

ENSG00000253968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377732	XR_001743001.1	n.3056+377C>A		intron_variant	Intron 14 of 14
LOC105377732	XR_007059057.1	n.4116+377C>A		intron_variant	Intron 17 of 17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253968	ENST00000827042.1	n.446+1595C>A		intron_variant	Intron 2 of 2
ENSG00000253968	ENST00000827044.1	n.374+1595C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55521 AN: 151892 Hom.: 10372 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.366 AC: 55591 AN: 152010 Hom.: 10395 Cov.: 32 AF XY: 0.369 AC XY: 27422 AN XY: 74302

African (AFR) AF: 0.293 AC: 12166 AN: 41462

American (AMR) AF: 0.463 AC: 7065 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1142 AN: 3470

East Asian (EAS) AF: 0.271 AC: 1404 AN: 5172

South Asian (SAS) AF: 0.404 AC: 1946 AN: 4822

European-Finnish (FIN) AF: 0.388 AC: 4094 AN: 10544

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26459 AN: 67958

Other (OTH) AF: 0.393 AC: 830 AN: 2114

Alfa AF: 0.389 Hom.: 5628

Bravo AF: 0.367

Asia WGS AF: 0.347 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.86
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs7722165; hg19: chr5-172934970; COSMIC: COSV60232125;