chr6-25600740-G-T

Variant names:

• chr6-25600740-G-T
• rs10456324
• NM_017640.6:c.3546G>T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_017640.6(CARMIL1):​c.3546G>T​(p.Ala1182Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000731 in 1,367,070 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 7.3e-7 (0 hom.)
• Consequence: CARMIL1 NM_017640.6 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 0 publications found

Genes affected

CARMIL1 (HGNC:21581): (capping protein regulator and myosin 1 linker 1) Involved in several processes, including actin filament network formation; plasma membrane bounded cell projection organization; and positive regulation of cellular component organization. Located in several cellular components, including lamellipodium; macropinosome; and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP7: Synonymous conserved (PhyloP=-1.6 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017640.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARMIL1	NM_017640.6	MANE Select	c.3546G>T	p.Ala1182Ala	synonymous	Exon 33 of 37	NP_060110.4
	CARMIL1	NM_001173977.2		c.3546G>T	p.Ala1182Ala	synonymous	Exon 33 of 37	NP_001167448.1	A0A8V8TRE2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARMIL1	ENST00000329474.7	TSL:1 MANE Select	c.3546G>T	p.Ala1182Ala	synonymous	Exon 33 of 37	ENSP00000331983.6	Q5VZK9-1
	CARMIL1	ENST00000865798.1		c.3546G>T	p.Ala1182Ala	synonymous	Exon 33 of 38	ENSP00000535857.1
	CARMIL1	ENST00000911480.1		c.3546G>T	p.Ala1182Ala	synonymous	Exon 34 of 38	ENSP00000581539.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.31e-7 AC: 1 AN: 1367070 Hom.: 0 Cov.: 36 AF XY: 0.00000149 AC XY: 1 AN XY: 670822

African (AFR) AF: 0.00 AC: 0 AN: 30242

American (AMR) AF: 0.00 AC: 0 AN: 27944

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20810

East Asian (EAS) AF: 0.00 AC: 0 AN: 38244

South Asian (SAS) AF: 0.00 AC: 0 AN: 70320

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 49744

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5352

European-Non Finnish (NFE) AF: 9.36e-7 AC: 1 AN: 1068022

Other (OTH) AF: 0.00 AC: 0 AN: 56392

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.079
DANN	Benign	0.32
PhyloP100		-1.6

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10456324; hg19: chr6-25600968;