rs1968201

Variant names:

• chr7-103166988-A-G
• rs1968201
• XM_047421168.1:c.*1827A>G

Variant summary

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

The XM_047421168.1(LOC105375434):​c.*1827A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0686 in 152,348 control chromosomes in the GnomAD database, including 461 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 0.069 (461 hom., cov: 32)
• Consequence: LOC105375434 XM_047421168.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 5 publications found

Genes affected

LOC105375434 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702099.1. 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
	ENSG00000289956	ENST00000702099.1		n.154+13915A>G		intron	N/A
	ENSG00000289956	ENST00000702842.2		n.269+13915A>G		intron	N/A
	ENSG00000289956	ENST00000838451.1		n.451-4259A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0686 AC: 10438 AN: 152230 Hom.: 460 Cov.: 32

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.0540

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0627

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0810

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0686 AC: 10445 AN: 152348 Hom.: 461 Cov.: 32 AF XY: 0.0698 AC XY: 5199 AN XY: 74512

African (AFR) AF: 0.0254 AC: 1057 AN: 41586

American (AMR) AF: 0.121 AC: 1856 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3470

East Asian (EAS) AF: 0.0533 AC: 277 AN: 5194

South Asian (SAS) AF: 0.132 AC: 637 AN: 4830

European-Finnish (FIN) AF: 0.0627 AC: 666 AN: 10624

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0810 AC: 5508 AN: 68018

Other (OTH) AF: 0.0654 AC: 138 AN: 2110

Alfa AF: 0.0786 Hom.: 153

Bravo AF: 0.0723

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.5
DANN	Benign	0.82
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1968201; hg19: chr7-102807435;