chr1-96983373-T-C

Variant names:

• chr1-96983373-T-C
• rs7529671
• ENST00000845412.1:n.180+195A>G

Variant summary

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

The ENST00000845412.1(ENSG00000309905):​n.180+195A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,160 control chromosomes in the GnomAD database, including 2,854 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 0.11 (2854 hom., cov: 32)
• Consequence: ENSG00000309905 ENST00000845412.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• Publications: 1 publications found

Genes affected

ENSG00000309905 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000845412.1. 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
	ENSG00000309905	ENST00000845412.1		n.180+195A>G		intron	N/A
	ENSG00000309905	ENST00000845413.1		n.130+12007A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16345 AN: 152042 Hom.: 2847 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0360

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.000471

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00356

Gnomad OTH AF: 0.0785

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

GnomAD4 genome AF: 0.108 AC: 16385 AN: 152160 Hom.: 2854 Cov.: 32 AF XY: 0.105 AC XY: 7797 AN XY: 74402

African (AFR) AF: 0.364 AC: 15072 AN: 41458

American (AMR) AF: 0.0359 AC: 549 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00432 AC: 15 AN: 3472

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5180

South Asian (SAS) AF: 0.0655 AC: 316 AN: 4828

European-Finnish (FIN) AF: 0.000471 AC: 5 AN: 10618

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00356 AC: 242 AN: 68006

Other (OTH) AF: 0.0777 AC: 164 AN: 2112

Alfa AF: 0.0484 Hom.: 554

Bravo AF: 0.121

Asia WGS AF: 0.0600 AC: 210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs7529671; hg19: chr1-97448929;